How do I make a molecular "cloth" which I can drop some objects onto?
Emitter sounds a little like over complicating things. Here was my process. 


Create a plane with ~20 subdivisions. Add vertices that will be pinned to a vertex group.
Enable cloth physics for plane and enable pinning with the vertex group that was created as option. 
Animate an object moving or add a rigid body that will collide with the cloth and enable collision in the physics tab. 
Create the molecular object (Smoothed sphere in our case) and parent it to the cloth plane object. 
In the Object tab of the properties find duplication. Choose verts or faces. Make sure both objects are in the same layer as it will only display if they are.